Argonne National Laboratory - Biologyhttp://www.anl.gov/topics/biology
enKomodo dragons provide insights into microbial health in captive animalshttp://www.anl.gov/external-resource/komodo-dragons-provide-insights-microbial-health-captive-animals
<a href="/external-resource/komodo-dragons-provide-insights-microbial-health-captive-animals" class="title-link">Komodo dragons provide insights into microbial health in captive animals</a><div class="field field-name-group-audience field-type-group field-label-above"><div class="field-label">Groups audience&nbsp;</div><div class="field-items"><div class="field-item even"><a href="http://www.anl.gov/">Argonne National Laboratory</a></div></div></div><div class="field field-name-field-external-resource-url field-type-link-field field-label-above"><div class="field-label">URL&nbsp;</div><div class="field-items"><div class="field-item even"><a href="http://military-technologies.net/2016/12/02/komodo-dragons-provide-insights-into-microbial-health-in-captive-animals/" target="_blank">Komodo dragons provide insights into microbial health in captive animals</a> </div></div></div><div class="field field-name-field-extres-source field-type-text field-label-above"><div class="field-label">Source&nbsp;</div><div class="field-items"><div class="field-item even">Military Technologies</div></div></div><div class="field field-name-field-extres-postdate field-type-datetime field-label-above"><div class="field-label">Post Date&nbsp;</div><div class="field-items"><div class="field-item even"><span class="date-display-single" property="dc:date" datatype="xsd:dateTime" content="2016-12-02T15:30:00-06:00">Friday, December 2, 2016 - 15:30</span></div></div></div><div class="field field-name-field-topic-term field-type-taxonomy-term-reference field-label-above"><div class="field-label">Topic&nbsp;</div><div class="field-items"><div class="field-item even"><a href="/topics/environment" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">Environment</a></div><div class="field-item odd"><a href="/topics/biology" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">Biology</a></div><div class="field-item even"><a href="/topics/environmental-biology" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">Environmental biology</a></div><div class="field-item odd"><a href="/topics/terrestrial-ecology" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">Terrestrial ecology</a></div></div></div>Fri, 02 Dec 2016 21:52:22 +0000jkoka@anl.gov165861 at http://www.anl.govKomodo dragons help researchers understand microbial health in captive animalshttp://www.anl.gov/external-resource/komodo-dragons-help-researchers-understand-microbial-health-captive-animals
<a href="/external-resource/komodo-dragons-help-researchers-understand-microbial-health-captive-animals" class="title-link">Komodo dragons help researchers understand microbial health in captive animals</a><div class="field field-name-group-audience field-type-group field-label-above"><div class="field-label">Groups audience&nbsp;</div><div class="field-items"><div class="field-item even"><a href="http://www.anl.gov/">Argonne National Laboratory</a></div></div></div><div class="field field-name-field-external-resource-url field-type-link-field field-label-above"><div class="field-label">URL&nbsp;</div><div class="field-items"><div class="field-item even"><a href="http://scienmag.com/komodo-dragons-help-researchers-understand-microbial-health-in-captive-animals/" target="_blank">Komodo dragons help researchers understand microbial health in captive animals</a> </div></div></div><div class="field field-name-field-extres-source field-type-text field-label-above"><div class="field-label">Source&nbsp;</div><div class="field-items"><div class="field-item even">ScienMag</div></div></div><div class="field field-name-field-extres-postdate field-type-datetime field-label-above"><div class="field-label">Post Date&nbsp;</div><div class="field-items"><div class="field-item even"><span class="date-display-single" property="dc:date" datatype="xsd:dateTime" content="2016-11-29T10:00:00-06:00">Tuesday, November 29, 2016 - 10:00</span></div></div></div><div class="field field-name-field-topic-term field-type-taxonomy-term-reference field-label-above"><div class="field-label">Topic&nbsp;</div><div class="field-items"><div class="field-item even"><a href="/topics/environment" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">Environment</a></div><div class="field-item odd"><a href="/topics/biology" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">Biology</a></div><div class="field-item even"><a href="/topics/environmental-biology" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">Environmental biology</a></div><div class="field-item odd"><a href="/topics/terrestrial-ecology" typeof="skos:Concept" property="rdfs:label skos:prefLabel" datatype="">Terrestrial ecology</a></div></div></div>Thu, 01 Dec 2016 16:04:31 +0000jkoka@anl.gov165816 at http://www.anl.gov Komodo dragons help researchers understand microbial health in captive animalshttp://www.anl.gov/articles/komodo-dragons-help-researchers-understand-microbial-health-captive-animals
<a href="/articles/komodo-dragons-help-researchers-understand-microbial-health-captive-animals" class="title-link"> Komodo dragons help researchers understand microbial health in captive animals</a><span class="field field-name-field-article-contributor field-type-node-reference field-label-hidden"><span class="field-items"><span class="field-item even">By <a href="/contributors/joan-koka">Joan Koka</a> &bull; </span></span></span><span class="extra-created">November 28, 2016</span><div class="field field-name-field-video field-type-video-embed-field field-label-hidden"><div class="field-items"><div class="field-item even">
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</div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even" property="content:encoded"><p>Humans and Komodo dragons, the largest lizards in the world, could not be more different. In the wild, these four-legged carnivores wander in solitude across islands in Indonesia, consuming large prey like deer and water buffalo. But when placed in a closed environment, Komodo dragons interact with their surroundings much in the same way humans do – at least on the microbial level – and researchers are using this knowledge to help them understand the health of animals in captivity.</p>
<p>Researchers at the University of California San Diego, the University of Colorado-Boulder, the University of Chicago and the U.S. Department of Energy’s (DOE’s) Argonne National Laboratory, are the first to identify similarities in the way in which Komodo dragons and humans and their pets share microbes within closed environments.</p>
<p>Their findings, published in <a href="http://msystems.asm.org/content/1/4/e00046-16" target="_blank">The American Society of Microbiology’s mSystems journal</a>, say that the pattern of microbial exchange is “likely circular in nature,” meaning that captive dragons contribute microbes to their environment, and reacquire these same microbes from their environment, repeating this exchange in an ongoing cycle without other external sources of microbial diversity.</p>
<blockquote><p><strong>“... we’re exploring new animal models to see if we can ask the same questions we would about humans and get answers in more rigorous, controlled ways.” </strong></p>
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<p>Researchers noticed this pattern after sampling the microbial communities found in the saliva, skin and feces of 37 Komodo dragons across 12 U.S. zoos as well as the environment of two of the 12 enclosures. They then compared these two sets of data to each other and to past studies of humans and pets. Statistical comparison revealed that, as with humans and pets in their homes, captive Komodo dragons transfer a significant source of bacteria and other microbes to their enclosures.</p>
<p>These findings are helping researchers better understand the relationship between captivity and microbial diversity and health, knowledge that could be key to improving the health of animals in the care of zookeepers, veterinarians and other caretakers.</p>
<p>“Regardless of whether you’re in a closed or open environment, there’s always a constant exchange of microbes between a host and their environment, and that constant exposure has impacts on health; for example it can lead to changes in a host’s immune system that help the host stave off pathogens,” said Argonne’s Jack Gilbert, an author of the study and the director of <a href="https://microbiome.uchicago.edu/" target="_blank">The Microbiome Center</a>, a joint Argonne, University of Chicago and Marine Biological Laboratory program.</p>
<p>“The problem is that the degree of exposure becomes limited when you put a host in captivity, and this change has unknown consequences on health,” he said, “which is exactly why we’re trying to learn more about it.”</p>
<p>Evidence from past studies suggests that animals in captivity experience diseases that are associated with or worsened by captivity. Collectively these studies, which have included green sea turtles, polar bears and monkeys, bring weight to the “hygiene hypothesis,” which theorizes that reduced exposure to microbes is contributing to the increase in autoimmune and allergic disease occurrence in Westernized nations.</p>
<p>“For some animals there are diseases that affect them but don’t affect their wild counterparts, or don’t affect their counterparts as severely, so it makes sense that people, as they spend less time outdoors, would be affected in the same ways,” said lead author Embriette Hyde, an assistant project scientist and project manager of the American Gut Project.</p>
<p>This study is the largest of its kind on captive Komodo dragons, and the first to investigate the microbial communities in the feces and skin of Komodo dragons. To date, no comparable studies of wild Komodo dragons have been conducted.</p>
<p>Researchers are, however, continuing to explore microbiome interactions using other animal models. Gilbert, along with a separate group of researchers, is studying these interactions in captive dolphins and their environment.</p>
<p>“Since it’s quite difficult to track microbial exposure on a daily basis, especially with humans - who move around a lot - we’re exploring new animal models to see if we can ask the same questions we would about humans and get answers in more rigorous, controlled ways,” Gilbert said.</p>
<p>Through such research, investigators are hoping to identify useful systems to simulate the interactions between an animal and its environment, and find out whether the interactions within a given system are comparable to how humans interact with their environment. Such answers can expand our knowledge of the microbial health of humans and animals alike, and lead to improvements in animal husbandry practices.<br />
This work was funded by the John S. Templeton Foundation, the Alfred P. Sloan Foundation, and Argonne’s Laboratory Directed Research and Development program.</p>
<p><strong><em>Argonne National Laboratory</em></strong><em> seeks solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by </em><a href="http://www.uchicagoargonnellc.org/" target="_blank"><em>UChicago Argonne, LLC</em></a><em> for the </em><a href="http://science.energy.gov/" target="_blank"><em>U.S. Department of Energy's Office of Science</em></a><em>.</em></p>
<p><strong><em>The U.S. Department of Energy's Office of Science</em></strong><em> is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit the </em><a href="http://science.energy.gov/" target="_blank"><em>Office of Science website</em></a><em>.</em></p>
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</div></div></div><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even" property="content:encoded"><p>Data is pouring into the hands of cancer researchers, thanks to improvements in imaging, models and understanding of genetics. Today the data from a single patient’s tumor in a clinical trial can add up to one terabyte — the equivalent of 130,000 books.</p>
<p>But we don’t yet have the tools to efficiently process the mountain of genetic data to make more precise predictions for therapy. And it’s needed: treating cancer remains a complex moving target. We can’t yet say precisely how a specific tumor will react to any given drug, and as a patient is treated, cancer cells can continue to evolve, making the initial therapy less effective.</p>
<p>Toward this goal, the U.S. Department of Energy (DOE) is partnering with the <a href="http://www.cancer.gov/" target="_blank">National Cancer Institute</a> in an “all-government” approach to fighting cancer. Part of this partnership is a three-year pilot project called the Joint Design of Advanced Computing Solutions for Cancer (JDACSC), which will use DOE supercomputing to build sophisticated computational models to facilitate breakthroughs in the fight against cancer on the molecular, patient and population levels.</p>
<blockquote><p><strong>“I really think we are at a unique place right now."</strong></p>
<p> </p>
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<p>The pilot builds on President Obama’s <a href="https://www.whitehouse.gov/precision-medicine" target="_blank">Precision Medicine Initiative</a> and Vice President Biden’s recent "<a href="https://www.whitehouse.gov/CancerMoonshot" target="_blank">Cancer Moonshot</a>” to transition cancer therapy away from a “one-size-fits-all” approach. Instead, the goal is to move toward individualized diagnosis and treatment that accommodates a patient’s unique body chemistry and genetics.</p>
<p>“Cancer researchers are very good at generating all types of data, from genomic data, proteomic data and imaging data,” said Warren Kibbe, director of the Center for Biomedical Informatics and Information Technology at the National Cancer Institute. “What we’re not really good at yet is integrating all that information into a consistent model and making predictions on how a tumor will respond to a given treatment.”</p>
<h4>CANDLE</h4>
<p>Key to this collaboration is a computational framework called the CANcer Distributed Learning Environment (<a href="http://www.anl.gov/articles/two-argonne-led-projects-among-398-million-first-round-exascale-computing-project-awards" target="_blank">CANDLE</a>). Over the years, many projects have amassed a huge volume of cancer data, including tumor genomes, patient data and experiments on potential drugs. CANDLE is designed to use machine-learning algorithms to find patterns in large datasets. Machine learning is a type of artificial intelligence that focuses on developing programs that can teach themselves to grow and change when presented with new data. These patterns offer insights that may ultimately result in improved treatment or guidance on new experiments.</p>
<p>To date, machine learning studies have produced computational models that estimate drug response for a singular data point — say, a certain mutation. Researchers working with CANDLE, however, envision a higher degree of complexity that integrates many types of information, such as drug interactions and specifics about a patient’s genealogy, as well as the tumor’s molecular characteristics and how its protein expression varies over time.</p>
<p>“The research community has collected thousands of experiments with hundreds of thousands of data points characterizing tumors and their response to the drugs,” said Rick Stevens, an associate laboratory director at the DOE’s Argonne National Laboratory and professor of computer science at the University of Chicago. “By working with the national laboratories, the National Cancer Institute can now finally scale and quantify the cancer problem.”</p>
<p>Using this computational architecture, participating labs — Argonne, Lawrence Livermore, Los Alamos and Oak Ridge national laboratories — will focus on three problems singled out by the National Cancer Institute as the biggest bottlenecks to advancing cancer research by launching three pilots. These are: understanding key protein interactions, predicting drug response and automating patient information extraction to inform treatment strategies.</p>
<p>Each pilot looks at cancer from a different scale. Lawrence Livermore drives the molecular-level pilot, Argonne leads the patient-level pilot, Oak Ridge undertakes the population-level pilot and Los Alamos looks at uncertainty quantification across all three pilots.</p>
<h4>Molecular level</h4>
<p>Thirty percent of all cancers exhibit mutations in the Ras family — a collection of proteins that help trigger cellular machinery to make new cells or kill old ones.</p>
<p>The molecular-level pilot work being led by Lawrence Livermore will use the CANDLE architecture to predict how these proteins behave on the top of cell membranes. Then they will apply this knowledge to what researchers describe as the “Ras pathway problem,” where glitches cause genes to remain stuck in the “on” position, leading to cancerous tumors.</p>
<p>Researchers want to produce highly complex simulations that describe how a protein moves and binds to specific locations on the cell membrane. They hope such insights can be applied to the millions of Ras pathways and dramatically enhance our understanding of how they work by predicting the likelihood that a signal will take a certain path.</p>
<h4>Patient level</h4>
<p>Cancer encompasses hundreds of diseases, each with thousands of possible causes. Thus, bringing precision to therapy selection for a specific patient is the goal of the Argonne-led patient-level pilot.</p>
<p>With the CANDLE platform, researchers at the <a href="http://www.alcf.anl.gov/" target="_blank">Argonne Leadership Computing Facility</a>, a DOE Office of Science User Facility, will develop predictive models that guide drug treatment choices for tumors based on a much wider assortment of data than currently used.</p>
<p>To do this, they will merge one type of computational model that uses data to predict phenomena with another model that uses data to explain them. The hope is that by merging these two methods, they will be able to migrate lessons learned from computer simulations to the research laboratory, where researchers test mice to verify the computer’s prediction of how a tumor will respond to a given therapy. </p>
<p>Researchers will also try to find mechanisms for how a particular tumor evades a therapy or develops resistance.</p>
<p>“Conceptually, that’s how we’re thinking the future of cancer therapies is going to move. Right now we don’t understand the biological implications of resistance well enough for any particular therapy to do a good job at predicting combinatorial therapies,” said Kibbe. “We think that simulation will allow us to do a much better job of predicting which combination of therapies would be most effective for a specific patient.”</p>
<h4>Population level</h4>
<p>At any one point in time, three to five percent of patients with cancer participate in a cancer clinical trial. And cataloguing all this data is still a manual task.</p>
<p>Oak Ridge will help the National Cancer Institute to scale its ability to monitor cancer patients across the country by automating the process of entering and extracting information. By applying natural language processing and machine learning algorithms to these millions of clinical reports, computers will be able to derive meaning from the notes that doctors and nurses write in their reports.</p>
<p>Once completed, this system would automatically analyze and extract information so that researchers can monitor country-wide outcomes, which can then inform treatment strategies for patients of different lifestyles, environments and cancer types.</p>
<p>Steps are being taken to de-identify data before population-level pilot data is shared with participating labs, Stevens said.</p>
<h4>Next steps</h4>
<p>Over the next three years, both the National Cancer Institute and DOE have a monumental task; but they have a plan.</p>
<p>The first year will focus on merging statistical models and building machine-learning methods that make the best of their ability to explain and predict phenomena. In the second year, computer scientists will have to computationally estimate how confident they are in those predictions, and in the final year, researchers will put all of these pieces together and integrate experimental design.</p>
<p>“I really think we are at a unique place right now. There are some unbelievably great conversations happening across government right now about how we work together and integrate these brand new tools to enable understanding of these basic processes,” said Kibbe. “And if we can really understand the interplay of mutations, normal biological processes and cancer, we have a much better chance of being able to interfere with — and end — cancer.”</p>
<p>As the pilots progress from the building and merging of computational models to testing them in the laboratory, Stevens admits that you’d have to be a little fearless to go after a problem like this.</p>
<p>“In my nearly 20 years of working in computational biology, I can say that this is a really hard problem and it’s not clear if we know how to do this,” said Stevens. “But what the Cancer Moonshot gives us all is the ability to show the world how DOE labs can work in collaboration with the National Cancer Institute in a way that hasn’t been done before.”</p>
<p>“With that level of collaboration, it starts to look like less of a far-off moonshot,” he said, “and more a problem that we have a real shot at addressing.”</p>
<p>Support for the initiative is provided by the U.S. Department of Energy’s Office of Science, the National Institutes of Health and the National Nuclear Security Administration.</p>
<p><strong><em>Argonne National Laboratory</em></strong><em> seeks solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by </em><a href="http://www.uchicagoargonnellc.org/" target="_blank"><em>UChicago Argonne, LLC</em></a><em> for the </em><a href="http://science.energy.gov/" target="_blank"><em>U.S. Department of Energy's Office of Science</em></a><em>.</em></p>
<p><strong><em>The U.S. Department of Energy's Office of Science</em></strong><em> is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit the </em><a href="http://science.energy.gov/" target="_blank"><em>Office of Science website</em></a><em>.</em></p>
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